Pseudomonas aeruginosa faces a fitness trade-off between mucosal colonization and antibiotic tolerance during airway infections

Pseudomonas aeruginosa causes antibiotic-resilient acute and chronic pneumonia, but the mechanisms by which it adapts to the airway environment are poorly understood. Here, we investigated P. aeruginosa pathoadaptive mechanisms in tissue-engineered human airway organoids. Using transposon sequencing in situ, we decoded how P. aeruginosa survives on the mucosal surface during antibiotic treatment. Biofilm formation emerged as a major driver of P. aeruginosa colonization. Mutants that extensively produce biofilms on mucus show limited exploratory behavior, which limits nutrient access, slowing down their growth. Conversely, biofilm-dwelling P. aeruginosa better tolerate antibiotics via biophysical mechanisms. Finally, biofilms can shelter less-tolerant but more cytotoxic strains, thereby contributing to genotypic heterogeneity. P. aeruginosa must therefore adapt to conflicting physical and biological selective pressures to initiate chronic infections.